1. New computer hardware, unadorned with such snares and delusions as an operating system, an HLL, or even assembler. Commonly used in the phrase "programming on the bare metal", which refers to the arduous work of bit bashing needed to create these basic tools for a new computer. Real bare-metal programming involves things like building boot PROMs and BIOS chips, implementing basic monitors used to test device drivers, and writing the assemblers that will be used to write the compiler back ends that will give the new computer a real development environment.
2. "Programming on the bare metal" is also used to describe a style of hand-hacking that relies on bit-level peculiarities of a particular hardware design, especially tricks for speed and space optimisation that rely on crocks such as overlapping instructions (or, as in the famous case described in The Story of Mel, interleaving of opcodes on a magnetic drum to minimise fetch delays due to the device's rotational latency). This sort of thing has become less common as the relative costs of programming time and computer resources have changed, but is still found in heavily constrained environments such as industrial embedded systems, and in the code of hackers who just can't let go of that low-level control. See Real Programmer.
In the world of personal computing, bare metal programming is often considered a Good Thing, or at least a necessary evil (because these computers have often been sufficiently slow and poorly designed to make it necessary; see ill-behaved). There, the term usually refers to bypassing the BIOS or OS interface and writing the application to directly access device registers and computer addresses. "To get 19.2 kilobaud on the serial port, you need to get down to the bare metal." People who can do this sort of thing well are held in high regard.